Create README.md

README.md

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+# MetaCompassv1.0
+Last updated: Sept 30th, 2015
+
+
+
+# REQUIREMENTS:
+GNU C/C++; Perl; BLAST; Bowtie 2
+
+
+
+# INSTALLATION:
+    git clone https://github.com/marbl/MetaCompass.git
+    cd MetaCompassv1.0
+    ./install.pl
+
+
+# USAGE
+RUN METACOMPASS:
+-- I have a set of metagenomic reads, and want to perform comparative assembly.
+
+    ./metacompass.pl -f/-q <input FASTA/FASTQ reads> [options] 
+
+
+-- I know the reference genomes, or I want to perform comparative assembly for a particular genome.
+
+    ./metacompass.pl -f/-q [input FASTA/FASTQ reads] -r [reference genomes in FASTA] [options]
+
+
+-- You can try MetaCompass on two test data sets.
+For a small data set assuming reference genomes are known:
+
+    ./metacompass.pl -f test/small.reads.fna -r test/small.refgeno.fna -o test1_out
+
+For a big data set assuming reference genomes are known:
+
+    ./metacompass.pl -f test/big.reads.fna -r test/big.refgeno.fna -o test2_out
+
+For a big data set assuming reference genomes are NOT known:
+
+    ./metacompass.pl -f test/big.reads.fna -o test3_out
+
+# Output:
+      Assembled contigs:
+                contigs_[iteration #].fasta
+      
+      Taxonomic profiling output from MetaPhyler:
+                mc.classification; mc.[species|genus|family|order|class|phylum].taxprof
+      
+      Selected Reference genomes:
+                mc.refseq.fasta